Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate CCNA_02494 CCNA_02494 3-oxoadipate enol-lactonase/4-carboxymuconolactone decarboxylase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Caulo:CCNA_02494 Length = 393 Score = 261 bits (667), Expect = 2e-74 Identities = 149/378 (39%), Positives = 218/378 (57%), Gaps = 8/378 (2%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 GAAD P++VLL S+G + S+ DP L+ + RV+ +D RGHG S AP G YS+ L++D Sbjct: 17 GAADKPLLVLLNSIGCDLSLHDPVTPLLTPDFRVLRIDTRGHGASDAPSGDYSLDLLADD 76 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134 VLA++D+ G A G S+GG IA L + AP RV +L L CT+ + +W +R A Sbjct: 77 VLAVMDAAGAAKATICGTSLGGMIAMALASRAPDRVEALVLACTSPAM-DSSSWEQRLAV 135 Query: 135 SRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTAD 194 R +G ++ +AV++R+FS+ PE V R + + +P+GY C A+ D Sbjct: 136 IRAEGLSAIVEAVMSRFFSDDFRALHPEVVETVRAGMLAQNPDGYCGCGAAIRDMALLDR 195 Query: 195 LSRISAPTLVIAGEEDPSTP-PSVMQILADGITEARFEVLSPAAHVANLEQ----AGAVT 249 L +I+APTLV+ G +D +TP + + AR V+ AAH+ +LE AGAV Sbjct: 196 LPKIAAPTLVLTGSKDVATPFEGHADRIVAAVPGARHAVIE-AAHLPSLEAPAAFAGAVR 254 Query: 250 ALLREHIVGAGYARGRRAAHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWG 309 L E + GA + + G+ RR +LGDA VD+S+A T FTA +Q ITR AW Sbjct: 255 GFLAEVLHGAAVSDAKAVLFEAGLVTRRRVLGDAWVDKSLAKRTAFTADYQAMITRYAWN 314 Query: 310 DIWSRPGLDHELRRLLTIAVLTAVGNEHELDMHIRAAL-RAGVDADTIGEVLLHTSVYAG 368 +IW RPGLDH RRLL +A+ ++ E +H+RA L + G D + EVL+ ++YAG Sbjct: 315 EIWGRPGLDHRTRRLLVLAICASLARWEEFRLHVRAGLEQGGFTQDELKEVLMQIAIYAG 374 Query: 369 VPNSNLGFALGKQALADL 386 VP +N F +++L Sbjct: 375 VPAANTAFTEAADVMSEL 392 Lambda K H 0.318 0.132 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 394 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate CCNA_02494 CCNA_02494 (3-oxoadipate enol-lactonase/4-carboxymuconolactone decarboxylase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02427.hmm # target sequence database: /tmp/gapView.10406.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02427 [M=251] Accession: TIGR02427 Description: protocat_pcaD: 3-oxoadipate enol-lactonase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-101 324.8 0.1 2.3e-101 324.4 0.1 1.1 1 lcl|FitnessBrowser__Caulo:CCNA_02494 CCNA_02494 3-oxoadipate enol-lac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02494 CCNA_02494 3-oxoadipate enol-lactonase/4-carboxymuconolactone decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 324.4 0.1 2.3e-101 2.3e-101 1 250 [. 10 257 .. 10 258 .. 0.99 Alignments for each domain: == domain 1 score: 324.4 bits; conditional E-value: 2.3e-101 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlall 73 r+++r++ga+ dkp+lvl+nS+G+dl+l+d+v++ lt+dfrvlr+D+rGHG+Sd+p+g+ys++ laddvla++ lcl|FitnessBrowser__Caulo:CCNA_02494 10 RIYWRTDGAA-DKPLLVLLNSIGCDLSLHDPVTPLLTPDFRVLRIDTRGHGASDAPSGDYSLDLLADDVLAVM 81 69********.************************************************************** PP TIGR02427 74 DalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwF 146 Da+g++ka++cG+SlGG+ia+aLa+r+pdrvealvl++t+ +++ +sWe+R+a++raeGl+a+++av++r+F lcl|FitnessBrowser__Caulo:CCNA_02494 82 DAAGAAKATICGTSLGGMIAMALASRAPDRVEALVLACTSPAMDS-SSWEQRLAVIRAEGLSAIVEAVMSRFF 153 ********************************************9.99************************* PP TIGR02427 147 tpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpe.lvreiadl 218 +++fr+ +p+ +e+vr+ +++q+p+gY++++aAird++l +rl +ia+Ptlv++G++D++tP+e ++++i+++ lcl|FitnessBrowser__Caulo:CCNA_02494 154 SDDFRALHPEVVETVRAGMLAQNPDGYCGCGAAIRDMALLDRLPKIAAPTLVLTGSKDVATPFEgHADRIVAA 226 ****************************************************************99******* PP TIGR02427 219 vpgarfaeieeaaHlpnleqpeafaallrdfl 250 vpgar+a+ie aaHlp+le+p+afa ++r+fl lcl|FitnessBrowser__Caulo:CCNA_02494 227 VPGARHAVIE-AAHLPSLEAPAAFAGAVRGFL 257 **********.********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (393 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.82 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory